LAP3

protein-coding

leucine aminopeptidase 3, the group of Aminopeptidases

Gene summary

Predicted to enable peptidase activity. Predicted to be involved in proteolysis. Located in several cellular components, including extracellular exosome; focal adhesion; and mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PEPS

MANE transcript

NM_015907.3

Inheritance

—

ClinVar variants

U:89B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr4:17,577,198-17,607,972

External References & Databases

Ensembl (ENSG00000002549)

Transcript & Mutation Effects

hg38 • Region Span ~30.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LAP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 86

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015907.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			86 clinvar	2 clinvar		88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	89	2	0	91

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015907.3	RefSeq	NP_056991.2	13	MANE Select
ENST00000226299.9	Ensembl	ENSP00000226299.4	13	MANE Select
ENST00000513105.1	Ensembl	ENSP00000424724.1	6	Standard
ENST00000606142.5	Ensembl	ENSP00000476028.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Arginine and proline metabolism - Homo sapiens (human)
Glutathione metabolism - Homo sapiens (human)

Biological Process

proteolysis

Molecular Function

aminopeptidase activity
metalloexopeptidase activity
manganese ion binding

Cellular Component

nucleus
nucleoplasm
trans-Golgi network
cytosol
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000226299
Coding exons: 13
Length: 30781
Individuals with no LoFs: 125657
Homozygous LoFs: 0
Heterozygous LoFs: 91
Defined: 125748
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	246	299	0.822	0.0000161	3386
Missense (PolyPhen)		89	125.69	0.7081		1363
Synonymous	-0.284	118	114	1.03	0.00000716	1014
Loss of Function	1.96	15	25.7	0.583	0.00000116	316

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0031	0.0031	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.;

Recessive Scores

pRec: 0.643

Intolerance Scores

LoFtool: 0.728
RVIS EVS: -0.51
RVIS percentile EVS: 21.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.993

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium